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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa04LNT0259000.1

CAATAAAAAAACCAACTGCACATAAACACATTAAACAAATGCCCGCACATATGCGTGGGCTATCTTCCTAGTTTCACAAAAGTCATATATATAAATCACGAGGCTGTTAAGACGCAAATGTCGACGGATCGGACATTATTCGGACTAGCTAGCGGATCTCTGATACATGAGGACAGACAGCTGCGTATAAATCGCTTAACTGCTAGGAGGTAGAGGCAGTGCGATATAGACAACCGGCAGCCTCATCGTCTCCCCATCCACCGCCTTGCCCATCAGCTTTTCGAAGTCTTCCGCAAAGTCGTCGTCGGCGCTGCCCTCCACCCTCTTGCTCCGCAGGAGGAACGAGTCGTCGCGCTGCAAGTTGGTCGGCGCGCTCGCCTGCGCTCGCGACGTCGCGACGATGTACCGCCTGGACCGCGGCTGCACGACGCCCCTGTCCGGCACCGCGCGGTACTTGGACTCGTCCACCTGCACGGCGAACGCCACGCGATCGGCGGACCTGTTCGTCAGCTGCAGCACGCAGGATACATCCCTGTCCTTCTCAAATGGGAAGCGCACCTCCAGAGGGTCGATCACAAGGCGCTCCGATTTACACCCAGCTGAGCTCTGGCCTATAAGTGCCTTCCTCACATTTTCTAACTCGTTCAGTTTATCAATAATCTCCCTCAGAGTAGGCCTTTTCTTTCGGTCGGGTTCTACACACCTTACAGCTATTTCGATGCATGTCTTGACTTCTAGGCTATCTGCCTCATGTGATGATGTATGACTCGAAATTTCCTGCATCCTCTTTTTCCATTTCTCTTGTACAGTATCAATAAATTGTTGGGGAGACATTTCAGCACTTGTAGAACGGCCCGATTGTCCTGCCATTATCTCTATGATTATAACACCCAAACTGAATACATCAAACTTCATTGAGATATGGCGTCTCTCAATGTATTCTGGCGGCATGTACCCAACTGTTCCAATAAAAGTTCTTGTCGTAAAAGTTTGTGTTGAACCAAAGAGTCTTGACAAACCGAAATCAGCAATTTTTGGCATTTTGTTCTCATCCAGTAATATATTAGCAGGTTTCAAGTCCAAATGAACAATTTGATCTTCTGGACGACCATTGTGAAGGTAATCTAAACCCTCACAAATCCCCTTGATTATTTTGTAACGTGTGTGCCAATCAAGTCCACATGTTTCATCAGAAAGATACTTGTCAAGGCTTCCACGGTGCAAATATTCGAAGCAAAGTGCTCTTTCTTCCATTCTAGAAAAATGGTAATCTCCATCCACCTTGATATGTTTGTGTCGTATTTCATAGCAGTATCCAACTAACCCTATAATATTCTTATGCTGGACCCTCATAAGGTTATTAAATTCTTTCTTAAATTGCACATCGTCCAGTCCTACCATTTGATGTAGCTTCTTGATAGCAATCTCTGTGTTATTTTCCAGTACTCCCTTGTAAACAACTCCATACCCACCACTGCCAACTTTGTGCTCCTCAGAGAAACCATTTGTAATTTCTTCTAACTTTTTGTATGTAAGGTCCACGGGCATCACTCTTGCATGCTCTAACGTGTTCTCCTTGTCATCCAT

Coding Potentia
Explanation CPC Score
noncoding -1.16365
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa04LNT0259000.1 4 17915728 A T
Osa04LNT0259000.1 4 17916201 G C
Osa04LNT0259000.1 4 17916464 T C
Osa04LNT0259000.1 4 17916043 A C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa04LNT0259000.1 osa-miR166c-5p Cleavage 5.0 17.317 1 20
Osa04LNT0259000.1 osa-miR164c Translation 4.5 14.966 1 21
Osa04LNT0259000.1 osa-miR164c Translation 5.0 11.394 1 21
Osa04LNT0259000.1 osa-miR166j-5p Cleavage 5.0 17.088 1 21
Osa04LNT0259000.1 osa-miR1854-5p Translation 4.5 18.671 1 21
Osa04LNT0259000.1 osa-miR1857-5p Translation 5.0 7.901 1 21
Osa04LNT0259000.1 osa-miR2868 Cleavage 5.0 11.905 1 20
Osa04LNT0259000.1 osa-miR2863b Cleavage 4.0 13.915 1 21
Osa04LNT0259000.1 osa-miR2929 Translation 4.5 17.145 1 21
Osa04LNT0259000.1 osa-miR2873b Cleavage 2.5 12.394 1 21
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa04LNT0259000.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259000.1 4 gwt4a Morphological trait Seed RG788 RG190
Osa04LNT0259000.1 4 nan Morphological trait Panicle/flower RG788 RZ69
Osa04LNT0259000.1 4 qNOT4-2 Resistance or Tolerance Drought tolerance RG449 RG788
Osa04LNT0259000.1 4 qFRP4-1 Physiological trait Source activity RG449 RG788
Osa04LNT0259000.1 4 An8-glum Morphological trait Panicle/flower nan nan
Osa04LNT0259000.1 4 nan Morphological trait Root RG449 RG788
Osa04LNT0259000.1 4 qCCFJ-4 Physiological trait Source activity RM261 RM3785
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus